Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 24 of 24
Found at i:4495015 original size:28 final size:27
Alignment explanation
Indices: 4494960--4495030 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
4494950 GCCACCCATA
4494960 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
4494987 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
4495015 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
4495031 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:4495148 original size:20 final size:20
Alignment explanation
Indices: 4495107--4495148 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4495097 AAATAGAGGC
* *
4495107 TCCCTCCTCCTTCTCATGTA
1 TCCCTCATCCTTCTCATATA
*
4495127 TCCCTCATCCTTCTCTTATA
1 TCCCTCATCCTTCTCATATA
4495147 TC
1 TC
4495149 TCTCTTCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.43, G:0.02, T:0.43
Consensus pattern (20 bp):
TCCCTCATCCTTCTCATATA
Found at i:4495654 original size:3 final size:3
Alignment explanation
Indices: 4495646--4495685 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4495636 TAATTATCTA
4495646 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4495686 GTTTGTATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4496746 original size:2 final size:2
Alignment explanation
Indices: 4496739--4496781 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
4496729 TTTTGAAAAT
4496739 TA TA TA TA TA TA TA TA TA T- TA -A TA -A TGA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
4496779 TA T
1 TA T
4496782 TGACATCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 32 0.86
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4497254 original size:12 final size:12
Alignment explanation
Indices: 4497237--4497261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4497227 TATATTGATC
4497237 ACATAAATATAA
1 ACATAAATATAA
4497249 ACATAAATATAA
1 ACATAAATATAA
4497261 A
1 A
4497262 TTATTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
ACATAAATATAA
Found at i:4497722 original size:23 final size:21
Alignment explanation
Indices: 4497694--4497738 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
4497684 ATATGTTTTA
4497694 ATATTTATATTATAATATGATAT
1 ATATTTAT-TT-TAATATGATAT
*
4497717 ATATTTATTTTTATATGATAT
1 ATATTTATTTTAATATGATAT
4497738 A
1 A
4497739 AATTACATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 2 0.10
23 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
ATATTTATTTTAATATGATAT
Found at i:4497755 original size:16 final size:16
Alignment explanation
Indices: 4497734--4497781 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
4497724 TTTTTATATG
4497734 ATATAAATTACATAAT-
1 ATATAAATTA-ATAATA
4497750 ATATAAATATAA-AATA
1 ATATAAAT-TAATAATA
4497766 ATATAAATTATATAAT
1 ATATAAATTA-ATAAT
4497782 TGAAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAATTAATAATA
Found at i:4500687 original size:20 final size:20
Alignment explanation
Indices: 4500664--4500703 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4500654 CATATTAAAA
4500664 TTTAAATA-TATATATAATAT
1 TTTAAATATTAT-TATAATAT
4500684 TTTAAATATTATTATAATAT
1 TTTAAATATTATTATAATAT
4500704 AAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATATTATTATAATAT
Found at i:4501345 original size:29 final size:28
Alignment explanation
Indices: 4501287--4501344 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
4501277 TAATATTTTT
*
4501287 ATATTTTTATTATTAAATTTAAATAAAA
1 ATATTTTTATTATTAAATGTAAATAAAA
4501315 ATATTTTTATTATTTAAATAGTAATATAAA
1 ATATTTTTATTA-TTAAAT-GTAA-ATAAA
4501345 TCCGACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.46
29 6 0.23
30 3 0.12
31 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
ATATTTTTATTATTAAATGTAAATAAAA
Found at i:4503190 original size:6 final size:7
Alignment explanation
Indices: 4503175--4503201 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4503165 CAAGCAAGGA
4503175 TTTTATT
1 TTTTATT
4503182 TTTTATT
1 TTTTATT
4503189 TTTTATT
1 TTTTATT
4503196 TTTTAT
1 TTTTAT
4503202 AACTGTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:4503430 original size:21 final size:19
Alignment explanation
Indices: 4503399--4503437 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
4503389 AGATTAATAA
*
4503399 TATAATTATATTTATTATG
1 TATAATTATATATATTATG
4503418 TATAATTTGATATATATTAT
1 TATAA-TT-ATATATATTAT
4503438 ATTAATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TATAATTATATATATTATG
Found at i:4504052 original size:4 final size:4
Alignment explanation
Indices: 4504043--4504070 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4504033 TATAAAGAAC
4504043 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
4504071 GTTTTGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:4504283 original size:27 final size:27
Alignment explanation
Indices: 4504248--4504304 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4504238 CTATTTTAAA
* * *
4504248 TATATTTAAATATTAAA-AAATTATTTT
1 TATAATTAAAT-TTAAATAAAATAATTT
4504275 TATAATTAAATTTAAATAAAATAATTT
1 TATAATTAAATTTAAATAAAATAATTT
4504302 TAT
1 TAT
4504305 TATCCATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATAATTAAATTTAAATAAAATAATTT
Found at i:4505039 original size:2 final size:2
Alignment explanation
Indices: 4505032--4505064 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4505022 TCTTTATGTG
4505032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4505065 CTTTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4513260 original size:17 final size:17
Alignment explanation
Indices: 4513240--4513282 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
4513230 TTTTAGAGTT
*
4513240 AAGTATAAATGTTTTTC
1 AAGTATAAATATTTTTC
4513257 AAGTATAAATATTTTTC
1 AAGTATAAATATTTTTC
*
4513274 AAGAATAAA
1 AAGTATAAA
4513283 AATAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (17 bp):
AAGTATAAATATTTTTC
Found at i:4513305 original size:20 final size:19
Alignment explanation
Indices: 4513251--4513308 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
4513241 AGTATAAATG
*
4513251 TTTTTCAAGT-ATAAAT-A
1 TTTTTCAAGTAAAAAATAA
*
4513268 TTTTTCAAGAATAAAAATAA
1 TTTTTCAAGTA-AAAAATAA
4513288 TATTTTCAAGTAAAAAATAA
1 T-TTTTCAAGTAAAAAATAA
4513308 T
1 T
4513309 CCAAAGTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 9 0.26
19 5 0.15
20 11 0.32
21 9 0.26
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTTTCAAGTAAAAAATAA
Found at i:4515123 original size:12 final size:12
Alignment explanation
Indices: 4515106--4515144 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
4515096 TCAACTATCA
4515106 AAGATGATGATG
1 AAGATGATGATG
4515118 AAGATGATGATG
1 AAGATGATGATG
*
4515130 ATA-ATGATGAAG
1 A-AGATGATGATG
4515142 AAG
1 AAG
4515145 TTGACTTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (12 bp):
AAGATGATGATG
Found at i:4515173 original size:17 final size:18
Alignment explanation
Indices: 4515133--4515173 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
4515123 GATGATGATA
*
4515133 ATGATGAAGAAGTTGACT
1 ATGATGAAGAAGATGACT
4515151 -TGGATGAAGAA-ATGACT
1 AT-GATGAAGAAGATGACT
4515168 ATGATG
1 ATGATG
4515174 GCTAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (18 bp):
ATGATGAAGAAGATGACT
Found at i:4521408 original size:16 final size:16
Alignment explanation
Indices: 4521387--4521422 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4521377 AAATTTGTAT
4521387 AAGGGGGAAAGATAAA
1 AAGGGGGAAAGATAAA
*
4521403 AAGGGGGAGAGATAAA
1 AAGGGGGAAAGATAAA
4521419 AAGG
1 AAGG
4521423 AAGAGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.06
Consensus pattern (16 bp):
AAGGGGGAAAGATAAA
Found at i:4522081 original size:20 final size:22
Alignment explanation
Indices: 4522039--4522084 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
4522029 AGTTAAGTAT
4522039 TAATGTTTTTCAAGCATAAAAA
1 TAATGTTTTTCAAGCATAAAAA
*
4522061 TAATG-TTTTCAAGTA-AAAAA
1 TAATGTTTTTCAAGCATAAAAA
4522081 TAAT
1 TAAT
4522085 CCAAAGTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
21 9 0.39
22 5 0.22
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
TAATGTTTTTCAAGCATAAAAA
Found at i:4523584 original size:17 final size:17
Alignment explanation
Indices: 4523553--4523602 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
4523543 TCTGTTAAAT
4523553 TAAAT-TATATATTTTTA
1 TAAATATATAT-TTTTTA
4523570 TAAATATATATTTTTTA
1 TAAATATATATTTTTTA
4523587 TAAATATATTATTTTT
1 TAAATATA-TATTTTT
4523603 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAAATATATATTTTTTA
Found at i:4523608 original size:23 final size:25
Alignment explanation
Indices: 4523582--4523633 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 25
4523572 AATATATATT
*
4523582 TTTTATAAATATATTAT-TTTT-AA
1 TTTTATAAATATATAATCTTTTAAA
4523605 -TTT-TAAATATATAATCTTTTAAA
1 TTTTATAAATATATAATCTTTTAAA
4523628 TTTTAT
1 TTTTAT
4523634 CATGCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 2 0.08
24 3 0.12
25 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTATAAATATATAATCTTTTAAA
Found at i:4523613 original size:21 final size:23
Alignment explanation
Indices: 4523587--4523632 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
4523577 ATATTTTTTA
*
4523587 TAAATATATTAT-TTTT-AATTT
1 TAAATATATAATCTTTTAAATTT
4523608 TAAATATATAATCTTTTAAATTT
1 TAAATATATAATCTTTTAAATTT
4523631 TA
1 TA
4523633 TCATGCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 4 0.18
23 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAATATATAATCTTTTAAATTT
Found at i:4524096 original size:16 final size:16
Alignment explanation
Indices: 4524075--4524110 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
4524065 TTAAATTTAA
4524075 ATAAAT-AATTTAATTT
1 ATAAATAAATTT-ATTT
4524091 ATAAATAAATTTATTT
1 ATAAATAAATTTATTT
4524107 ATAA
1 ATAA
4524111 CGAACCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATAAATTTATTT
Found at i:4524320 original size:29 final size:26
Alignment explanation
Indices: 4524241--4524328 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 26
4524231 AAAAATTTTT
* * *
4524241 ATTTTATTATTTTTAAAGAAACTTTTAA
1 ATTTTATTATATTTAAATAAA-TATT-A
*
4524269 ATTTTATTATATTTAAATGAATATTTA
1 ATTTTATTATATTTAAATAAATA-TTA
4524296 ATTTTAATATATATTTAAATAAATATTA
1 ATTTT-AT-TATATTTAAATAAATATTA
4524324 ATTTT
1 ATTTT
4524329 TAATTTAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
27 7 0.13
28 30 0.58
29 15 0.29
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTTATTATATTTAAATAAATATTA
Found at i:4524329 original size:29 final size:28
Alignment explanation
Indices: 4524297--4524395 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 28
4524287 GAATATTTAA
4524297 TTTTAATATATATTTAA-ATAAATATTAAT
1 TTTTAATATATATTTAACATAAATA--AAT
* *
4524326 TTTTAATTTA-ATTTATACATAAAGAAAT
1 TTTTAATATATATTTA-ACATAAATAAAT
* * *
4524354 TTTTATTATTTAATTTAACTTTAAATAAAT
1 TTTTAATATAT-ATTTAAC-ATAAATAAAT
4524384 TTTTAATATATA
1 TTTTAATATATA
4524396 ATTTTTATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
28 15 0.27
29 13 0.23
30 28 0.50
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (28 bp):
TTTTAATATATATTTAACATAAATAAAT
Found at i:4524370 original size:35 final size:35
Alignment explanation
Indices: 4524290--4524376 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 35
4524280 TTTAAATGAA
* ** *
4524290 TATTTAATTTTAATATATATTTAAATAAATATTAAT
1 TATTTAA-TTTAATTTATACATAAAGAAATATTAAT
* *
4524326 T-TTTAATTTAATTTATACATAAAGAAATTTTTAT
1 TATTTAATTTAATTTATACATAAAGAAATATTAAT
4524360 TATTTAATTTAACTTTA
1 TATTTAATTTAA-TTTA
4524377 AATAAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
34 23 0.53
35 15 0.35
36 5 0.12
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (35 bp):
TATTTAATTTAATTTATACATAAAGAAATATTAAT
Found at i:4524407 original size:30 final size:29
Alignment explanation
Indices: 4524323--4524407 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 29
4524313 AATAAATATT
* **
4524323 AATTTTTAAT-TTAATTTATACATAAAGA
1 AATTTTTAATATTAATTTTTATTTAAAGA
* * *
4524351 AATTTTTATTATTTAA-TTTAACTTTAAATA
1 AATTTTTAATA-TTAATTTTTA-TTTAAAGA
4524381 AATTTTTAATATATAATTTTTATTTAA
1 AATTTTTAATAT-TAATTTTTATTTAA
4524408 GGATTCATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
28 9 0.20
29 4 0.09
30 27 0.61
31 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (29 bp):
AATTTTTAATATTAATTTTTATTTAAAGA
Found at i:4524583 original size:25 final size:24
Alignment explanation
Indices: 4524550--4524599 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
4524540 ACCGCATCAT
4524550 ATCAATCAAAGAG-TGCAGCAAATA
1 ATCAATCAAAGAGTTG-AGCAAATA
*
4524574 ATCAGATCAAGGAGTTGAGCAAATA
1 ATCA-ATCAAAGAGTTGAGCAAATA
4524599 A
1 A
4524600 AAAAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 17 0.74
26 2 0.09
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (24 bp):
ATCAATCAAAGAGTTGAGCAAATA
Found at i:4534502 original size:22 final size:24
Alignment explanation
Indices: 4534470--4534522 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
4534460 TTATAGTTAA
* *
4534470 ATATTTAAATTTATAATTA-TA-T
1 ATATTTTAATTAATAATTATTATT
*
4534492 ATATTTTAATTAATATTTATTATT
1 ATATTTTAATTAATAATTATTATT
4534516 ATATTTT
1 ATATTTT
4534523 TGAGATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 16 0.62
23 2 0.08
24 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTTTAATTAATAATTATTATT
Found at i:4544634 original size:76 final size:76
Alignment explanation
Indices: 4544542--4544694 Score: 270
Period size: 76 Copynumber: 2.0 Consensus size: 76
4544532 TCATGCATAT
*
4544542 ATTTAAGTTTAATTTTATTTTTTATCACATATTATTTGTTGATATAAAATTTAATATTTAATATG
1 ATTTAAGTTTAATTTTATTTTTTATCACATATTATTTATTGATATAAAATTTAATATTTAATATG
4544607 ATATTAAAGTC
66 ATATTAAAGTC
* * *
4544618 ATTTAAGTTTAATTTTATTTTTTATCACGTATTATTTATTTATATTAAATTTAATATTTAATATG
1 ATTTAAGTTTAATTTTATTTTTTATCACATATTATTTATTGATATAAAATTTAATATTTAATATG
4544683 ATATTAAAGTC
66 ATATTAAAGTC
4544694 A
1 A
4544695 AAAGAATAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (76 bp):
ATTTAAGTTTAATTTTATTTTTTATCACATATTATTTATTGATATAAAATTTAATATTTAATATG
ATATTAAAGTC
Found at i:4544659 original size:37 final size:37
Alignment explanation
Indices: 4544541--4544659 Score: 89
Period size: 37 Copynumber: 3.2 Consensus size: 37
4544531 ATCATGCATA
*
4544541 TATTTAAGTTTAATTTTATTTTTTATCACATATTATT
1 TATTTAAGTTTAATTTTATTTTTTATCACGTATTATT
* * ** * * * * *
4544578 TGTTGATA-TAAAATTTAATATTTAAT-ATGATATTAAAGT
1 TATTTA-AGTTTAATTTTATTTTTTATCACG-TATT--ATT
*
4544617 CATTTAAGTTTAATTTTATTTTTTATCACGTATTATT
1 TATTTAAGTTTAATTTTATTTTTTATCACGTATTATT
4544654 TATTTA
1 TATTTA
4544660 TATTAAATTT
Statistics
Matches: 55, Mismatches: 21, Indels: 12
0.62 0.24 0.14
Matches are distributed among these distances:
36 1 0.02
37 28 0.51
38 2 0.04
39 22 0.40
40 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (37 bp):
TATTTAAGTTTAATTTTATTTTTTATCACGTATTATT
Found at i:4544688 original size:37 final size:37
Alignment explanation
Indices: 4544570--4544688 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
4544560 TTTTTATCAC
* * *
4544570 ATATTATTTGTTGATATAAAATTTAATATTTAATATG
1 ATATTATTTATTTATATTAAATTTAATATTTAATATG
* * * * * * *
4544607 ATATTAAAGTCATTTA-AGTTTAATTTTATTTTTTATCACG
1 ATATT--ATTTATTTATA-TTAAATTTAATATTTAAT-ATG
4544647 -TATTATTTATTTATATTAAATTTAATATTTAATATG
1 ATATTATTTATTTATATTAAATTTAATATTTAATATG
4544683 ATATTA
1 ATATTA
4544689 AAGTCAAAAG
Statistics
Matches: 59, Mismatches: 17, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
36 2 0.03
37 31 0.53
38 2 0.03
39 22 0.37
40 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (37 bp):
ATATTATTTATTTATATTAAATTTAATATTTAATATG
Found at i:4545575 original size:13 final size:13
Alignment explanation
Indices: 4545541--4545576 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4545531 TTAATTTTTA
**
4545541 AAATTAATCGTAT
1 AAATTAATTATAT
4545554 AAATTAATTATAT
1 AAATTAATTATAT
4545567 AAATTAATTA
1 AAATTAATTA
4545577 AAATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (13 bp):
AAATTAATTATAT
Found at i:4545726 original size:19 final size:21
Alignment explanation
Indices: 4545702--4545740 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
4545692 ATATTGAATT
*
4545702 AAATAATA-TTATTT-TATTA
1 AAATAAAATTTATTTATATTA
4545721 AAATAAAATTTATTTATATT
1 AAATAAAATTTATTTATATT
4545741 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAAAATTTATTTATATTA
Found at i:4549355 original size:17 final size:17
Alignment explanation
Indices: 4549333--4549370 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
4549323 ATTTTCCGGT
*
4549333 TCCGTGGCATTTGGTCC
1 TCCGTGGCATCTGGTCC
4549350 TCCGTGGCATCTGGTCC
1 TCCGTGGCATCTGGTCC
4549367 TCCG
1 TCCG
4549371 CTGTGGCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.34, G:0.29, T:0.32
Consensus pattern (17 bp):
TCCGTGGCATCTGGTCC
Found at i:4555147 original size:32 final size:32
Alignment explanation
Indices: 4555106--4555169 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
4555096 TGTGATTCCT
*
4555106 TGTTGGTTGGTTGCTACGACTAGGTCCAACCG
1 TGTTGGTTGGTTGCTACCACTAGGTCCAACCG
4555138 TGTTGGTTGGTTGCTACCACTAGGTCCAACCG
1 TGTTGGTTGGTTGCTACCACTAGGTCCAACCG
4555170 AAGGGTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.31
Consensus pattern (32 bp):
TGTTGGTTGGTTGCTACCACTAGGTCCAACCG
Found at i:4557026 original size:22 final size:22
Alignment explanation
Indices: 4556995--4557065 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 22
4556985 TTTTATATTT
4556995 TTAATAATTTTTATATAATTTATA
1 TTAAT-ATTTTTATATAA-TTATA
*
4557019 TT-ATATTTAGTTA-ATTATTATA
1 TTAATATTT--TTATATAATTATA
*
4557041 TTAATTTTATTTATATAAATTATA
1 TTAATATT-TTTATAT-AATTATA
4557065 T
1 T
4557066 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
22 14 0.37
23 11 0.29
24 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (22 bp):
TTAATATTTTTATATAATTATA
Found at i:4557046 original size:32 final size:30
Alignment explanation
Indices: 4556975--4557056 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
4556965 ATAATATAAA
* *
4556975 ATTAAATTAATTTTA-TATTTTTAATAATT
1 ATTATATTAATTTTATTATATTTAATAATT
* *
4557004 TTTATA-TAATTTATATTATATTTAGTTAATT
1 ATTATATTAATTT-TATTATATTTA-ATAATT
4557035 ATTATATTAATTTTATTTATAT
1 ATTATATTAATTTTA-TTATAT
4557057 AAATTATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 6 0.14
29 6 0.14
30 7 0.16
31 12 0.28
32 12 0.28
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (30 bp):
ATTATATTAATTTTATTATATTTAATAATT
Found at i:4557075 original size:14 final size:14
Alignment explanation
Indices: 4557056--4557126 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
4557046 TTTATTTATA
4557056 TAAATTATATATTT
1 TAAATTATATATTT
*
4557070 TAAATT-TA-A--A
1 TAAATTATATATTT
* *
4557080 TAAATTAAAAATATT
1 TAAATTATATAT-TT
4557095 T-AATTATATATTT
1 TAAATTATATATTT
* *
4557108 TATATAATATATTT
1 TAAATTATATATTT
4557122 TAAAT
1 TAAAT
4557127 AATTAAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
10 6 0.14
11 1 0.02
12 2 0.05
13 5 0.12
14 28 0.65
15 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAAATTATATATTT
Found at i:4557112 original size:47 final size:45
Alignment explanation
Indices: 4557046--4557135 Score: 108
Period size: 47 Copynumber: 2.0 Consensus size: 45
4557036 TTATATTAAT
* * *
4557046 TTTATTTATATAAATTATATATTTTAAATTTAAATAAATTAAAAATA
1 TTTAATTATATAAATTATATAATAT-AATTTAAAT-AATTAAAAATA
** *
4557093 TTTAATTATATATTTTATATAATATATTTTAAATAATTAAAAA
1 TTTAATTATATAAATTATATAATATAATTTAAATAATTAAAAA
4557136 AATAATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
45 9 0.24
46 8 0.22
47 20 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (45 bp):
TTTAATTATATAAATTATATAATATAATTTAAATAATTAAAAATA
Found at i:4557116 original size:24 final size:24
Alignment explanation
Indices: 4557005--4557117 Score: 76
Period size: 24 Copynumber: 4.8 Consensus size: 24
4556995 TTAATAATTT
* * *
4557005 TTATATAATTTATATTATATTTAG
1 TTATATAAATTATATAATATTTAA
* *
4557029 TTA-AT-TATTATATTAAT-TTTAT
1 TTATATAAATTATA-TAATATTTAA
4557051 TTATATAAATTATAT-AT-TTTAAA
1 TTATATAAATTATATAATATTT-AA
* *
4557074 TTTAAATAAATTA-AAAATATTTAA
1 -TTATATAAATTATATAATATTTAA
**
4557098 TTATATATTTTATATAATAT
1 TTATATAAATTATATAATAT
4557118 ATTTTAAATA
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
22 17 0.25
23 19 0.28
24 30 0.43
25 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
TTATATAAATTATATAATATTTAA
Found at i:4558534 original size:2 final size:2
Alignment explanation
Indices: 4558522--4558562 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4558512 TGGAATCGGG
*
4558522 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4558563 GTTTTTACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4559835 original size:3 final size:3
Alignment explanation
Indices: 4559827--4559855 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4559817 TGCAGTGTCC
4559827 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4559856 TACGTAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4562724 original size:22 final size:22
Alignment explanation
Indices: 4562699--4562753 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
4562689 AATAAATTAA
4562699 AATATTAAAAATATTTTAT-ATT
1 AATATT-AAAATATTTTATAATT
*
4562721 AATATTTAAATATTTTATAATT
1 AATATTAAAATATTTTATAATT
*
4562743 AA-ATTTAAATA
1 AATATTAAAATA
4562754 AAATATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTAAAATATTTTATAATT
Found at i:4562733 original size:21 final size:21
Alignment explanation
Indices: 4562707--4562753 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
4562697 AAAATATTAA
4562707 AAATATTTTAT-ATTAATATTT
1 AAATATTTTATAATTAA-ATTT
4562728 AAATATTTTATAATTAAATTT
1 AAATATTTTATAATTAAATTT
4562749 AAATA
1 AAATA
4562754 AAATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATTTTATAATTAAATTT
Found at i:4563994 original size:34 final size:34
Alignment explanation
Indices: 4563968--4564036 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
4563958 AAATAATTAA
4563968 CTCATAAAAAATGCCGAAAACAATAAAATGGAAG
1 CTCATAAAAAATGCCGAAAACAATAAAATGGAAG
*
4564002 CTCATAAAAAATGCCGAAAACAAGAAAATGGAAG
1 CTCATAAAAAATGCCGAAAACAATAAAATGGAAG
4564036 C
1 C
4564037 AAACAAGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (34 bp):
CTCATAAAAAATGCCGAAAACAATAAAATGGAAG
Found at i:4565400 original size:9 final size:9
Alignment explanation
Indices: 4565386--4565428 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
4565376 AATTAAATAT
4565386 TTAATTTAA
1 TTAATTTAA
4565395 TTAATTAATAA
1 TTAATT--TAA
*
4565406 TTATTTTAA
1 TTAATTTAA
*
4565415 TTAATTAAA
1 TTAATTTAA
4565424 TTAAT
1 TTAAT
4565429 AATTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 21 0.72
11 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTAATTTAA
Found at i:4565413 original size:20 final size:20
Alignment explanation
Indices: 4565376--4565422 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
4565366 TCTACTATTA
*
4565376 AATTAAATATTTAATTTAATT
1 AATT-AATAATTAATTTAATT
*
4565397 AATTAATAATTATTTTAATT
1 AATTAATAATTAATTTAATT
4565417 AATTAA
1 AATTAA
4565423 ATTAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTAATAATTAATTTAATT
Found at i:4565439 original size:25 final size:25
Alignment explanation
Indices: 4565385--4565432 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
4565375 AAATTAAATA
4565385 TTTAATTTAATTAATTAATAATTAT
1 TTTAATTTAATTAATTAATAATTAT
4565410 TTTAA-TTAATTAAATTAATAATT
1 TTTAATTTAATT-AATTAATAATT
4565433 TTATTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTAATTTAATTAATTAATAATTAT
Found at i:4565936 original size:2 final size:2
Alignment explanation
Indices: 4565929--4565959 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4565919 GAATTTATCT
4565929 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4565960 GGGCGTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4566701 original size:21 final size:21
Alignment explanation
Indices: 4566652--4566701 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4566642 TTAAATTTTT
4566652 ATTATATATGAATTTAATCTA
1 ATTATATATGAATTTAATCTA
* * *
4566673 GTTTTATATTGAATTTATTC-A
1 ATTATATA-TGAATTTAATCTA
4566694 ATTATATA
1 ATTATATA
4566702 ATATTGATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTATATATGAATTTAATCTA
Found at i:4568036 original size:25 final size:27
Alignment explanation
Indices: 4567987--4568039 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4567977 TGAATTTAAT
4567987 TATTTTTTTAAATCATATTTAATTATA
1 TATTTTTTTAAATCATATTTAATTATA
*
4568014 TATTTTTTTACATCA-ATTT-ATTATA
1 TATTTTTTTAAATCATATTTAATTATA
4568039 T
1 T
4568040 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 14 0.56
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (27 bp):
TATTTTTTTAAATCATATTTAATTATA
Found at i:4569331 original size:24 final size:25
Alignment explanation
Indices: 4569274--4569332 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
4569264 TTACGTTAAA
4569274 ATTTTAA-ATATTAATATAACATGT
1 ATTTTAATATATTAATATAACATGT
* *
4569298 ATATTAAATATATT-ATATTA-ATGAT
1 AT-TTTAATATATTAATATAACATG-T
4569323 ATTTTAATAT
1 ATTTTAATAT
4569333 GATGTGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 12 0.41
25 12 0.41
26 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (25 bp):
ATTTTAATATATTAATATAACATGT
Found at i:4570348 original size:2 final size:2
Alignment explanation
Indices: 4570341--4570401 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
4570331 CAAATGGGCC
*
4570341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4570383 AT AT TT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
4570402 CACACACCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4570689 original size:10 final size:9
Alignment explanation
Indices: 4570676--4570720 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
4570666 GTTTAATTTT
4570676 AAAATTAATA
1 AAAATTAA-A
4570686 AAAATTAAA
1 AAAATTAAA
* *
4570695 TAAATTTAA
1 AAAATTAAA
*
4570704 AAAATTTAA
1 AAAATTAAA
4570713 AAAATTAA
1 AAAATTAA
4570721 TTGAATAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:4570707 original size:19 final size:20
Alignment explanation
Indices: 4570675--4570718 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4570665 GGTTTAATTT
*
4570675 TAAAATTAATAAAAATTAAA
1 TAAATTTAATAAAAATTAAA
*
4570695 TAAATTTAA-AAAATTTAAA
1 TAAATTTAATAAAAATTAAA
4570714 -AAATT
1 TAAATT
4570719 AATTGAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 9 0.41
20 8 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATTTAATAAAAATTAAA
Found at i:4571333 original size:6 final size:6
Alignment explanation
Indices: 4571322--4571384 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
4571312 TTTCGAAGTG
* * * *
4571322 ATATAT ATATAT ATATA- AT-TAT ATTTAT ATTTAT ATATTT ATATTT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
4571368 ATATAT ATATAA ATATA
1 ATATAT ATATAT ATATA
4571385 AAGATTAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
4 2 0.04
5 4 0.08
6 45 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATATAT
Found at i:4571333 original size:8 final size:8
Alignment explanation
Indices: 4571322--4571384 Score: 67
Period size: 8 Copynumber: 8.1 Consensus size: 8
4571312 TTTCGAAGTG
4571322 ATATATAT
1 ATATATAT
4571330 ATATATAT
1 ATATATAT
4571338 A-AT-TAT
1 ATATATAT
*
4571344 ATTTATAT
1 ATATATAT
*
4571352 TTATATAT
1 ATATATAT
* *
4571360 TTATATTT
1 ATATATAT
4571368 ATATATAT
1 ATATATAT
*
4571376 ATAAATAT
1 ATATATAT
4571384 A
1 A
4571385 AAGATTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
6 4 0.09
7 3 0.07
8 39 0.85
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
ATATATAT
Found at i:4571350 original size:14 final size:14
Alignment explanation
Indices: 4571327--4571384 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
4571317 AAGTGATATA
4571327 TATATATATATAAT
1 TATATATATATAAT
*
4571341 TATAT-T-TATATT
1 TATATATATATAAT
* *
4571353 TATATATTTATATT
1 TATATATATATAAT
*
4571367 TATATATATATAAA
1 TATATATATATAAT
4571381 TATA
1 TATA
4571385 AAGATTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
14 26 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATATATATAAT
Found at i:4571422 original size:17 final size:16
Alignment explanation
Indices: 4571399--4571432 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4571389 TTAAATATAT
*
4571399 ATTTAAAATAATAAAA
1 ATTTTAAATAATAAAA
*
4571415 ATTTTAAATAATATAA
1 ATTTTAAATAATAAAA
4571431 AT
1 AT
4571433 ATATATTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTTAAATAATAAAA
Found at i:4571719 original size:25 final size:26
Alignment explanation
Indices: 4571677--4571728 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
4571667 ATTATTAATG
*
4571677 AATTATAAATAATTAAATAAATATAA
1 AATTATAAATAATTAAATAAAAATAA
*
4571703 AATTTTAAA-AATTAAATAAAAATAA
1 AATTATAAATAATTAAATAAAAATAA
4571728 A
1 A
4571729 TGTATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AATTATAAATAATTAAATAAAAATAA
Found at i:4573311 original size:2 final size:2
Alignment explanation
Indices: 4573304--4573351 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4573294 AAAGCAGGAA
4573304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4573346 AT AT AT
1 AT AT AT
4573352 TGCGGTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4579123 original size:17 final size:17
Alignment explanation
Indices: 4579096--4579128 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4579086 AATCCAAAGC
4579096 CTTATCAATATCACCTTG
1 CTTATCAATATC-CCTTG
4579114 CTTA-CAATATCCCTT
1 CTTATCAATATCCCTT
4579129 CATTAAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.39
Consensus pattern (17 bp):
CTTATCAATATCCCTTG
Found at i:4587036 original size:36 final size:35
Alignment explanation
Indices: 4586996--4587108 Score: 154
Period size: 36 Copynumber: 3.1 Consensus size: 35
4586986 ACTTTCGAGA
**
4586996 AGAAGCAGAAGCAGAAGTCCTGCAAGATCTTCTAGG
1 AGAAGCATTAGCAGAAGTCCTG-AAGATCTTCTAGG
*
4587032 AGAAGCATTAGCAGAAGTCCCAGAAGATCTTCTAGG
1 AGAAGCATTAGCAGAAGT-CCTGAAGATCTTCTAGG
* *
4587068 AGAAGCATTAGTAGAAGTCCTGTAAGATCTTCTCGG
1 AGAAGCATTAGCAGAAGTCCTG-AAGATCTTCTAGG
4587104 AGAAG
1 AGAAG
4587109 TATAAGTAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 3 0.04
36 63 0.91
37 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (35 bp):
AGAAGCATTAGCAGAAGTCCTGAAGATCTTCTAGG
Found at i:4589006 original size:2 final size:2
Alignment explanation
Indices: 4589001--4589047 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4588991 ACACACACAC
4589001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4589043 AT AT A
1 AT AT A
4589048 AACAAAGACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4589241 original size:18 final size:18
Alignment explanation
Indices: 4589218--4589255 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4589208 TTATTACGTA
*
4589218 TTTTTATTTTTATTATAT
1 TTTTTATTTTTAATATAT
4589236 TTTTTATTTTTAATATAT
1 TTTTTATTTTTAATATAT
4589254 TT
1 TT
4589256 AATTATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATTTTTAATATAT
Found at i:4589379 original size:24 final size:23
Alignment explanation
Indices: 4589347--4589400 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
4589337 TTAAAATATT
*
4589347 TTAAAATATTTTTTTATATTAATA
1 TTAAAATATTTTTATA-ATTAATA
*
4589371 TTAATATATTTTTATAATTAA-A
1 TTAAAATATTTTTATAATTAATA
*
4589393 TTTAAATA
1 TTAAAATA
4589401 AAAATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAAATATTTTTATAATTAATA
Found at i:4590310 original size:2 final size:2
Alignment explanation
Indices: 4590303--4590331 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4590293 AAAATAACAT
4590303 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4590332 TTCACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4590935 original size:20 final size:20
Alignment explanation
Indices: 4590898--4590936 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4590888 TTAAAATTTA
*
4590898 TATTTTAATATTTTATTTTT
1 TATTTTAATATTTAATTTTT
4590918 TATTTTAA-ATTATAATTTT
1 TATTTTAATATT-TAATTTT
4590937 AAAATATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTAATATTTAATTTTT
Found at i:4591448 original size:4 final size:4
Alignment explanation
Indices: 4591439--4591466 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4591429 TTTATGATTG
4591439 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
4591467 TGAAAAACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:4591851 original size:15 final size:16
Alignment explanation
Indices: 4591831--4591863 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4591821 AAAGAATAAG
*
4591831 AATAA-TAAAACAATT
1 AATAATTAAAAAAATT
4591846 AATAATTAAAAAAATT
1 AATAATTAAAAAAATT
4591862 AA
1 AA
4591864 ATTAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAATTAAAAAAATT
Found at i:4592309 original size:27 final size:27
Alignment explanation
Indices: 4592270--4592329 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
4592260 TCAAATTAAT
4592270 TAAATTTAGTTTAAATTAATATAATTA
1 TAAATTTAGTTTAAATTAATATAATTA
* *
4592297 TAAATATTA-TTTAATTTAATTTAATT-
1 TAAAT-TTAGTTTAAATTAATATAATTA
4592323 T-AATTTA
1 TAAATTTA
4592330 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.10
25 3 0.10
26 1 0.03
27 20 0.67
28 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TAAATTTAGTTTAAATTAATATAATTA
Found at i:4592328 original size:5 final size:5
Alignment explanation
Indices: 4592265--4592330 Score: 62
Period size: 5 Copynumber: 12.8 Consensus size: 5
4592255 TCAATTCAAA
* * * *
4592265 TTAAT TAAAT TTAGT TTAAA TTAAT ATAAT TATAAAT ATT-AT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T-T-AAT -TTAAT TTAAT
4592312 TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAA
4592331 AAAATAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
4 2 0.04
5 41 0.84
6 1 0.02
7 4 0.08
8 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (5 bp):
TTAAT
Found at i:4592342 original size:42 final size:43
Alignment explanation
Indices: 4592265--4592348 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 43
4592255 TCAATTCAAA
* * *
4592265 TTAATTAAATTTAGTTTAAATTAATATAATTAT-AAATATTAT
1 TTAATTAAATTTAATTTAAATTAATAAAATAATAAAATATTAT
* *
4592307 TTAATTTAATTTAATTTAATTTAA-AAAATAAATAAAATATTA
1 TTAATTAAATTTAATTTAAATTAATAAAAT-AATAAAATATTA
4592349 CAAATTAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.11
42 23 0.66
43 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (43 bp):
TTAATTAAATTTAATTTAAATTAATAAAATAATAAAATATTAT
Found at i:4592955 original size:3 final size:3
Alignment explanation
Indices: 4592947--4592973 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4592937 AAAAACTTAA
4592947 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
4592974 TTACAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4593285 original size:2 final size:2
Alignment explanation
Indices: 4593274--4593309 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4593264 TTGAGTAAAG
4593274 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4593310 CTGAGTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4596025 original size:11 final size:11
Alignment explanation
Indices: 4596009--4596034 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4595999 TGGATATCTC
4596009 TTTTTTTATTT
1 TTTTTTTATTT
4596020 TTTTTTTATTT
1 TTTTTTTATTT
4596031 TTTT
1 TTTT
4596035 GGTGTTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:4599213 original size:20 final size:22
Alignment explanation
Indices: 4599190--4599233 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
4599180 AAATGAATTT
*
4599190 ATTAA-AA-TATTTTTATTTAA
1 ATTAATAATTATTATTATTTAA
4599210 ATTAATTAATTATTATTATTTAA
1 ATTAA-TAATTATTATTATTTAA
4599233 A
1 A
4599234 AATTTAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAATAATTATTATTATTTAA
Found at i:4608475 original size:2 final size:2
Alignment explanation
Indices: 4608468--4608500 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4608458 AGAGCAAATC
4608468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4608501 AAATACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4609567 original size:19 final size:19
Alignment explanation
Indices: 4609543--4609584 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
4609533 TTAAAAAATA
4609543 TTTATATCTAATATATATT
1 TTTATATCTAATATATATT
*
4609562 TTTATATCTAATTTATATT
1 TTTATATCTAATATATATT
4609581 TTTA
1 TTTA
4609585 AGAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATCTAATATATATT
Found at i:4609777 original size:16 final size:16
Alignment explanation
Indices: 4609756--4609793 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
4609746 CCATCAAGCA
4609756 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
4609772 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
*
4609788 TTTTTA
1 ATTTTA
4609794 TTTAAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:4611577 original size:13 final size:13
Alignment explanation
Indices: 4611561--4611596 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
4611551 TTAATTATAT
4611561 TAAATATTAATAA
1 TAAATATTAATAA
4611574 TAAATATTAATAA
1 TAAATATTAATAA
*
4611587 TAAAAATTAA
1 TAAATATTAA
4611597 AATTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATATTAATAA
Found at i:4614731 original size:22 final size:22
Alignment explanation
Indices: 4614704--4614749 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4614694 ATTATTTTAA
*
4614704 AAATT-AATTATATAAATTAATT
1 AAATTAAATTAT-GAAATTAATT
*
4614726 AAATTAAATTCTGAAATTAATT
1 AAATTAAATTATGAAATTAATT
4614748 AA
1 AA
4614750 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATTAAATTATGAAATTAATT
Found at i:4616789 original size:41 final size:39
Alignment explanation
Indices: 4616724--4616805 Score: 112
Period size: 41 Copynumber: 2.1 Consensus size: 39
4616714 GATGCCAAAG
4616724 TAAAATATAAATATAATATAATATAATTT-TTAAAGGTAT
1 TAAAATATAAATATAATATAATAT-ATTTATTAAAGGTAT
* *
4616763 TAAAATTATAAATATGAATATTATATATTTATTAAATGTAT
1 TAAAA-TATAAATAT-AATATAATATATTTATTAAAGGTAT
4616804 TA
1 TA
4616806 TATTAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 5 0.13
40 13 0.34
41 20 0.53
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (39 bp):
TAAAATATAAATATAATATAATATATTTATTAAAGGTAT
Found at i:4616860 original size:41 final size:42
Alignment explanation
Indices: 4616784--4616877 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 42
4616774 ATATGAATAT
* *
4616784 TATATATTTATTAAATGTATTATATTAATTATA-TT-TTAAA
1 TATATTTTTATTAAATGTATTATAGTAATTATATTTATTAAA
* * * * *
4616824 TGTAATTTTTATTAAATTTTTTATAGTATTTTTATTTATTAAA
1 TAT-ATTTTTATTAAATGTATTATAGTAATTATATTTATTAAA
4616867 TATATTTTTAT
1 TATATTTTTAT
4616878 ATTTTTTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.05
41 24 0.56
42 10 0.23
43 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (42 bp):
TATATTTTTATTAAATGTATTATAGTAATTATATTTATTAAA
Found at i:4619546 original size:2 final size:2
Alignment explanation
Indices: 4619539--4619569 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4619529 CGAATATGTG
*
4619539 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4619570 GCTCCCCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4621883 original size:22 final size:22
Alignment explanation
Indices: 4621858--4621910 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
4621848 TTTTTAAAAA
*
4621858 TAAATAATCTAATTCAATCAAT-
1 TAAATAATCTAAATCAAT-AATC
4621880 TAAATCAAT-TAAATCAATAATC
1 TAAAT-AATCTAAATCAATAATC
4621902 TAAA-AATCT
1 TAAATAATCT
4621911 CATTGATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 4 0.15
22 17 0.63
23 3 0.11
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATAATCTAAATCAATAATC
Found at i:4621885 original size:9 final size:9
Alignment explanation
Indices: 4621863--4621897 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4621853 AAAAATAAAT
*
4621863 AATCTAATTC
1 AATC-AATTA
4621873 AATCAATTA
1 AATCAATTA
4621882 AATCAATTA
1 AATCAATTA
4621891 AATCAAT
1 AATCAAT
4621898 AATCTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (9 bp):
AATCAATTA
Found at i:4623200 original size:25 final size:25
Alignment explanation
Indices: 4623166--4623219 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
4623156 TTGAATTAAA
4623166 TTTTAAAATTATTTAAATAATAGAT
1 TTTTAAAATTATTTAAATAATAGAT
4623191 TTTTAAAATTATTTAAATAATAGAT
1 TTTTAAAATTATTTAAATAATAGAT
4623216 TTTT
1 TTTT
4623220 CTGTACAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTTAAAATTATTTAAATAATAGAT
Found at i:4627084 original size:14 final size:14
Alignment explanation
Indices: 4627065--4627091 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4627055 AATGAAAATT
4627065 TTATTTTTATATTA
1 TTATTTTTATATTA
4627079 TTATTTTTATATT
1 TTATTTTTATATT
4627092 TTTTATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTTTATATTA
Found at i:4627264 original size:16 final size:17
Alignment explanation
Indices: 4627233--4627271 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
4627223 ATAAATTAAC
*
4627233 ATTTCATTTGAAATAAAT
1 ATTT-ATTTGAAATAAAA
4627251 ATTTATTT-AAATAAAA
1 ATTTATTTGAAATAAAA
4627267 ATTTA
1 ATTTA
4627272 ATGCAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 4 0.20
18 4 0.20
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
ATTTATTTGAAATAAAA
Found at i:4627792 original size:29 final size:27
Alignment explanation
Indices: 4627731--4627793 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
4627721 ATTTATATAT
* *
4627731 TTTTATATTTTATAATTATATTTAAAA
1 TTTTATATATTATAATTAAATTTAAAA
*
4627758 TATTATATATT-TAATTAAATTTTAATAGA
1 TTTTATATATTATAATTAAA-TTTAA-A-A
4627787 TTTTATA
1 TTTTATA
4627794 ATATGTTACG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 14 0.48
28 1 0.03
29 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTATATATTATAATTAAATTTAAAA
Found at i:4629289 original size:14 final size:14
Alignment explanation
Indices: 4629219--4629291 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
4629209 TAAATATTAA
4629219 AAAATAAATATATT
1 AAAATAAATATATT
* * * *
4629233 -ATATCAATTTATA
1 AAAATAAATATATT
4629246 AAAATAAATATAATT
1 AAAATAAATAT-ATT
* *
4629261 AATATGAAT-TAATT
1 AAAATAAATAT-ATT
*
4629275 AAAATTAATATATT
1 AAAATAAATATATT
4629289 AAA
1 AAA
4629292 TATTTAAAAC
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
13 9 0.20
14 25 0.57
15 10 0.23
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (14 bp):
AAAATAAATATATT
Found at i:4629294 original size:29 final size:28
Alignment explanation
Indices: 4629218--4629290 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
4629208 TTAAATATTA
*
4629218 AAAAATAAATATATT-ATATCAATTTAT
1 AAAAATAAATATATTAATATCAATTAAT
*
4629245 AAAAATAAATATAATTAATATGAATTAAT
1 AAAAATAAATAT-ATTAATATCAATTAAT
* *
4629274 TAAAATTAATATATTAA
1 AAAAATAAATATATTAA
4629291 ATATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 12 0.30
28 8 0.20
29 20 0.50
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (28 bp):
AAAAATAAATATATTAATATCAATTAAT
Found at i:4629753 original size:18 final size:19
Alignment explanation
Indices: 4629723--4629762 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4629713 TTTTCATAAT
4629723 AAATGATATAA-TTTTTTA
1 AAATGATATAATTTTTTTA
4629741 AAAT-ATATAAATTTTTTTA
1 AAATGATAT-AATTTTTTTA
4629760 AAA
1 AAA
4629763 AATTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATGATATAATTTTTTTA
Found at i:4629772 original size:19 final size:19
Alignment explanation
Indices: 4629734--4629769 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4629724 AATGATATAA
*
4629734 TTTTTTAAAATATATAAAT
1 TTTTTTAAAAAATATAAAT
4629753 TTTTTTAAAAAAT-TAAA
1 TTTTTTAAAAAATATAAA
4629770 ATTAATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTTAAAAAATATAAAT
Found at i:4629926 original size:20 final size:20
Alignment explanation
Indices: 4629890--4629936 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
4629880 AAATTAAAAA
4629890 TAATATTAAATAAATATATT
1 TAATATTAAATAAATATATT
* *
4629910 TAAT-TT-AATATATATATA
1 TAATATTAAATAAATATATT
4629928 T-ATATTAAA
1 TAATATTAAA
4629937 ATGATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 4 0.17
20 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATTAAATAAATATATT
Found at i:4629935 original size:18 final size:17
Alignment explanation
Indices: 4629877--4629936 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 17
4629867 TATGTACAAA
*
4629877 ATTAAATTAAAAATA-AT
1 ATTAAA-TAAATATATAT
*
4629894 ATTAAATAAATATATTT
1 ATTAAATAAATATATAT
*
4629911 AATTTAATATATATATATAT
1 -A-TTAA-ATAAATATATAT
4629931 ATTAAA
1 ATTAAA
4629937 ATGATAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.20
17 8 0.23
18 5 0.14
19 5 0.14
20 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAAATAAATATATAT
Found at i:4630565 original size:15 final size:15
Alignment explanation
Indices: 4630541--4630578 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4630531 GTCCAATAAT
4630541 AAAT-AAATAAAAAC
1 AAATAAAATAAAAAC
*
4630555 AAATAAAATAAAACC
1 AAATAAAATAAAAAC
*
4630570 AAAGAAAAT
1 AAATAAAAT
4630579 CTCTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:4633209 original size:3 final size:3
Alignment explanation
Indices: 4633201--4633229 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4633191 AAGCATGTGT
4633201 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4633230 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4633593 original size:18 final size:17
Alignment explanation
Indices: 4633552--4633591 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4633542 TAAAATTATG
*
4633552 AAAAAATAAAAATAATT
1 AAAAAAGAAAAATAATT
* *
4633569 ATAAAAGAAAAATATTT
1 AAAAAAGAAAAATAATT
4633586 AAAAAA
1 AAAAAA
4633592 AGTTAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAAAGAAAAATAATT
Done.